Markers + reference

Silene

29 species · Caryophyllaceae · Caryophyllales

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Species 29
Genome length 147–161 kb
Candidate markers 268
Primer pairs 75

Genome-wide nucleotide diversity

Sliding-window nucleotide diversity
Sliding-window nucleotide diversity (π) across the plastome.

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
accD LSC 1938 0.1201 0.74 72.3 yes View details
clpP1 LSC 2031 0.0697 0.99 80.9 yes View details
trnN-GUU-ycf1 IRb 356 0.1118 0.79 60.1 yes View details
ycf1 IRb 1863 0.1217 0.70 65.9 yes View details
ycf1 SSC 5886 0.0563 0.93 75.5 no View details
ycf1-trnN-GUU IRa 356 0.1094 0.82 61.4 yes View details
rps16-trnQ-UUG LSC 696 0.0519 0.96 85.8 yes View details
rpl32-trnL-UAG SSC 868 0.0622 0.95 82.4 yes View details
psbK-psbI LSC 439 0.0473 0.97 81.7 yes View details
petA-psbJ LSC 963 0.0431 0.98 81.6 yes View details
ndhC-trnV-UAC LSC 1115 0.0447 0.92 81.3 yes View details
psaA-ycf3 LSC 994 0.0541 0.94 80.9 yes View details
petN-psbM LSC 549 0.0425 0.96 80.2 yes View details
ndhF-rpl32 SSC 763 0.0472 0.97 80.2 yes View details
trnK-UUU-rps16 LSC 661 0.0656 0.90 79.4 yes View details
trnE-UUC-trnT-GGU LSC 556 0.0443 0.98 79.2 yes View details
Candidate markers include all hotspot labels marked in the diversity plot, listed in genomic order, plus the top 10 remaining regions by MarkerSeek score. Primer design is attempted for every listed region. Primer available: yes means at least one valid primer pair was found; no means no valid pair passed screening; NA means primer design was skipped.

Primer pairs

Showing the top 30 of 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAAAAGGCGCTCAACCTACA 80–913 1.000 90.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAAAAGGCGCTCAACCTACA 80–912 1.000 90.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GCCGTACGAGGAGAAAACTT 80–1192 1.000 90.0
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GCCGTACGAGGAGAAAACTT 80–1191 1.000 90.0
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TCTATCCCAATGAGCCGTCT 80–985 0.966 88.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 80–810 1.000 90.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 80–821 1.000 89.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCATCGGGTTTTGGTC 80–840 1.000 89.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC TAAGGCATCGGGTTTTGGTC 80–851 1.000 89.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA ATAGAAATCGAAGTGGGGCG 80–871 1.000 89.0
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACGCCCCGGATCATTAGATA 80–618 1.000 91.0
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG TACGCCCCGGATCATTAGAT 80–619 1.000 91.0
psbK-psbI_p3 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTACGCCCCGGATCATTAGA 80–620 1.000 89.2
psbK-psbI_p4 psbK-psbI TGGCAAGCTGCTGTAAGTTT ACGCCCCGGATCATTAGATA 80–615 1.000 89.0
psbK-psbI_p5 psbK-psbI TGGCAAGCTGCTGTAAGTTT TACGCCCCGGATCATTAGAT 80–616 1.000 89.0
petN-psbM_p1 petN-psbM ATTGTAAGTCTCGCTTGGGC AAAACGGTCAGCCAAAATGA 80–694 0.966 76.1
petN-psbM_p2 petN-psbM ATGGGGAAGAAGTGGACTCT AAAACGGTCAGCCAAAATGA 80–632 0.966 75.4
petN-psbM_p3 petN-psbM ATTGTAAGTCTCGCTTGGGC AAACGGTCAGCCAAAATGAT 80–693 0.966 74.2
petN-psbM_p4 petN-psbM ATTGTAAGTCTCGCTTGGGC AACGGTCAGCCAAAATGATT 80–692 0.966 74.2
petN-psbM_p5 petN-psbM ATTGTAAGTCTCGCTTGGGC AAAAACGGTCAGCCAAAATGA 80–695 0.966 74.1
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA ACTCTATTCCGCGTGCAAAT 80–778 0.966 89.3
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA CCATGGCGTTACTCTACCAC 80–687 0.966 88.9
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA GAACCGATGACTTACGCCTT 80–710 0.931 88.0
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA GAACCGATGACTTACGCCTT 80–708 0.931 88.0
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA ACTCTATTCCGCGTGCAAAT 80–780 0.931 87.9
psaA-ycf3_p1 psaA-ycf3 GGCACTAGGTCCAATGTGAG ATTGCAGAGGCTTGGTTTGA 80–1639 1.000 91.8
psaA-ycf3_p2 psaA-ycf3 GGCACTAGGTCCAATGTGAG TGAAATTGCAGAGGCTTGGT 80–1643 1.000 91.8
psaA-ycf3_p3 psaA-ycf3 GGCACTAGGTCCAATGTGAG TTGCAGAGGCTTGGTTTGAT 80–1638 1.000 91.8
psaA-ycf3_p4 psaA-ycf3 GCATCAGCATGTAGGTTCCA ATTGCAGAGGCTTGGTTTGA 80–1461 1.000 91.7
psaA-ycf3_p5 psaA-ycf3 GCATCAGCATGTAGGTTCCA TTGCAGAGGCTTGGTTTGAT 80–1460 1.000 91.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (29)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Silene acaulis subsp. acaulis PP190929.1 151910 View on NCBI ↗
Silene alexandrae NC_077503.1 150632 View on NCBI ↗
Silene aprica NC_040934.1 150293 View on NCBI ↗
Silene asclepiadea NC_061183.1 152162 View on NCBI ↗
Silene atrocastanea NC_061184.1 149945 View on NCBI ↗
Silene atsaensis NC_069859.1 150052 View on NCBI ↗
Silene caespitella NC_069860.1 149971 View on NCBI ↗
Silene capitata NC_035226.1 150224 View on NCBI ↗
Silene chodatii NC_061185.1 150105 View on NCBI ↗
Silene coronaria PQ533855.1 150358 View on NCBI ↗
Silene delavayi NC_061186.1 150482 View on NCBI ↗
Silene dioica PP190930.1 150983 View on NCBI ↗
Silene firma NC_087617.1 150242 View on NCBI ↗
Silene flos-cuculi subsp. flos-cuculi PP165055.1 146611 View on NCBI ↗
Silene gonosperma NC_077502.1 150158 View on NCBI ↗
Silene gracilicaulis NC_061187.1 152470 View on NCBI ↗
Silene latifolia NC_016730.1 151736 View on NCBI ↗
Silene latifolia subsp. alba MN244687.1 151747 View on NCBI ↗
Silene lhassana NC_069861.1 151919 View on NCBI ↗
Silene lineariloba NC_061188.1 149261 View on NCBI ↗
Silene melanantha NC_061189.1 150145 View on NCBI ↗
Silene nana NC_077499.1 151214 View on NCBI ↗
Silene olgiana NC_077498.1 161184 View on NCBI ↗
Silene repens NC_077497.1 154362 View on NCBI ↗
Silene stewartiana NC_061190.1 149859 View on NCBI ↗
Silene tatarinowii NC_061191.1 152111 View on NCBI ↗
Silene viscidula NC_061192.1 151866 View on NCBI ↗
Silene vulgaris NC_016727.1 151583 View on NCBI ↗
Silene vulgaris subsp. vulgaris MK473866.1 151572 View on NCBI ↗